Table 2

Mismatch discrimination for various primer designs at the SMAD7 rs4939827 SNP locus

3'-Primer Sequences

Cq values


(T/T)

(C/C)

ΔCq


...AA

26.0

26.0

0.0

...AA

    C

28.0

26.0

2.0

...AA

    T

25.8

26.7

0.9

...AA

    C
A

28.2

26.1

2.1

...AA

    T
A

25.6

26.1

0.5

...AA

    C
aGGAC-x

27.9

26.7

1.3

...AA

    T
aGGAC-x

26.9

26.4

0.5

...AAcAGGA-x

38.7

26.6

12.1

...AAuAGGA-x

27.9

40.5

12.6

...Aa

    C
AGG-x

36.4

27.5

8.8

...Aa

    T
AGG-x

26.2

28.8

2.6


Amplification reactions were performed in real-time mode using SYBR® Green detection and either homozygous C/C or homozygous T/T human genomic DNA. Reactions were run in triplicate; average Cq values are shown. ΔCq represents the difference between the Cq value for the mismatched reaction minus the Cq value for the matched reaction. Sequences at the 3'-end of the primers are shown. DNA bases are uppercase and RNA bases are bold lowercase. The C3 spacer blocking group is indicated by "x". The location of the mismatch in the primer compared to the target nucleic acid is underlined.

Dobosy et al. BMC Biotechnology 2011 11:80   doi:10.1186/1472-6750-11-80

Open Data